Fill the volume area of a bounding box with a grouping of individual meshes
How to use the particle emitter to create hexagonal fills.

Create a Cylinder with 6 sides as your Hexagon and define a Plane as the level shape. (I did try this with a 3D mesh but it is a bit more tricky to get everything lined up).


Add an Emitter and set the Object to be your Cylinder and the size to 0.5


Set the Emitter End to 1(so everything is done in frame 1) the Emit From to Faces and Grid, then you can check the box Hexagonal Grid. The Resolution needs to be tweaked here to get the fit of hexagons correct.



Then on the Modifiers panel click Convert to make the particles real.


and you can delete the original Plane and source Cylinder and manipulate the individual Cylinders.